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European Journal of Human Genetics: EJHG

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https://www.readbyqxmd.com/read/30006632/expanding-the-phenotypic-spectrum-of-variants-in-pde4d-prkar1a-from-acrodysostosis-to-acroscyphodysplasia
#1
Caroline Michot, Carine Le Goff, Edward Blair, Patricia Blanchet, Yline Capri, Brigitte Gilbert-Dussardier, Alice Goldenberg, Alex Henderson, Bertrand Isidor, Hulya Kayserili, Esther Kinning, Martine Le Merrer, Stanislas Lyonnet, Sylvie Odent, Pelin Ozlem Simsek-Kiper, Chloé Quelin, Ravi Savarirayan, Marleen Simon, Miranda Splitt, Judith M A Verhagen, Alain Verloes, Arnold Munnich, Geneviève Baujat, Valérie Cormier-Daire
Acrodysostosis (MIM 101800) is a dominantly inherited condition associating (1) skeletal features (short stature, facial dysostosis, and brachydactyly with cone-shaped epiphyses), (2) resistance to hormones and (3) possible intellectual disability. Acroscyphodysplasia (MIM 250215) is characterized by growth retardation, brachydactyly, and knee epiphyses embedded in cup-shaped metaphyses. We and others have identified PDE4D or PRKAR1A variants in acrodysostosis; PDE4D variants have been reported in three cases of acroscyphodysplasia...
July 13, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30002500/before-progressing-from-exomes-to-genomes-%C3%A2-don-t-forget-splicing-variants
#2
REVIEW
Samiha S Shaikh, Michael S Nahorski, Harjeet Rai, C Geoffrey Woods
No abstract text is available yet for this article.
July 12, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/30002499/human-urine-derived-renal-epithelial-cells-provide-insights-into-kidney-specific-alternate-splicing-variants
#3
Elisa Molinari, Eva Decker, Holly Mabillard, James Tellez, Shalabh Srivastava, Shreya Raman, Katrina Wood, Caroline Kempf, Sumaya Alkanderi, Simon A Ramsbottom, Colin G Miles, Colin A Johnson, Friedhelm Hildebrandt, Carsten Bergmann, John A Sayer
The majority of multi-exon genes undergo alternative splicing to produce different mRNA transcripts and this may occur in a tissue-specific manner. Assessment of mRNA transcripts isolated from blood samples may sometimes be unhelpful in determining the affect on function of putative splice-site variants affecting kidney-specific mRNA transcripts. Here we present data demonstrating the power of using human urine-derived renal epithelial cells (hUREC) as a source of kidney RNA. We report clinical and molecular genetic data from three affected cases from two families all with end-stage renal disease by 15 years of age...
July 12, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29995845/inferring-biogeographic-ancestry-with-compound-markers-of-slow-and-fast-evolving-polymorphisms
#4
Amandine Moriot, Carla Santos, Ana Freire-Aradas, Christopher Phillips, Diana Hall
Bio-geographic ancestry is an area of considerable interest in the medical genetics, anthropology and forensics. Although genome-wide panels are ideal as they provide dense genotyping data, small sets of ancestry informative marker provide a cost-effective way to investigate genetic ancestry and population structure. Here, we investigate the performance of a reduced marker set that combine different types of autosomal markers through haplotype analysis. In particular, recently described DIP-STR markers should offer the advantage of comprising both, low mutation rate Indels (DIPs), to study human history over longer time scale; and high mutation rate STRs, to trace relatively recent demographic events...
July 11, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29995844/molecular-genetic-overlap-between-migraine-and-major-depressive-disorder
#5
Yuanhao Yang, Huiying Zhao, Dorret I Boomsma, Lannie Ligthart, Andrea C Belin, George Davey Smith, Tonu Esko, Tobias M Freilinger, Thomas Folkmann Hansen, M Arfan Ikram, Mikko Kallela, Christian Kubisch, Christofidou Paraskevi, David P Strachan, Maija Wessman, Arn M J M van den Maagdenberg, Gisela M Terwindt, Dale R Nyholt
Migraine and major depressive disorder (MDD) are common brain disorders that frequently co-occur. Despite epidemiological evidence that migraine and MDD share a genetic basis, their overlap at the molecular genetic level has not been thoroughly investigated. Using single-nucleotide polymorphism (SNP) and gene-based analysis of genome-wide association study (GWAS) genotype data, we found significant genetic overlap across the two disorders. LD Score regression revealed a significant SNP-based heritability for both migraine (h2  = 12%) and MDD (h2  = 19%), and a significant cross-disorder genetic correlation (rG  = 0...
July 11, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29991739/paternal-origin-of-paleo-indians-in-siberia-insights-from-y-chromosome-sequences
#6
Lan-Hai Wei, Ling-Xiang Wang, Shao-Qing Wen, Shi Yan, Rebekah Canada, Vladimir Gurianov, Yun-Zhi Huang, Swapan Mallick, Alessandro Biondo, Amy O'Leary, Chuan-Chao Wang, Yan Lu, Chao Zhang, Li Jin, Shuhua Xu, Hui Li
The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous...
July 10, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29988065/lack-of-evidence-for-a-causal-role-of-calr3-in-monogenic-cardiomyopathy
#7
Judith M A Verhagen, Job H Veldman, Paul A van der Zwaag, Jan H von der Thüsen, Erwin Brosens, Imke Christiaans, Dennis Dooijes, Apollonia T J M Helderman-van den Enden, Ronald H Lekanne Deprez, Michelle Michels, Anneke M van Mil, Rogier A Oldenburg, Jasper J van der Smagt, Arthur van den Wijngaard, Marja W Wessels, Robert M W Hofstra, Marjon A van Slegtenhorst, Jan D H Jongbloed, Ingrid M B H van de Laar
The pathogenicity of previously published disease-associated genes and variants is sometimes questionable. Large-scale, population-based sequencing studies have uncovered numerous false assignments of pathogenicity. Misinterpretation of sequence variants may have serious implications for the patients and families involved, as genetic test results are increasingly being used in medical decision making. In this study, we assessed the role of the calreticulin-3 gene (CALR3) in cardiomyopathy. CALR3 has been included in several cardiomyopathy gene panels worldwide...
July 9, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29980747/correction-patient-experience-and-utility-of-genetic-information-a-cross-sectional-study-among-patients-tested-for-cancer-susceptibility-and-thrombophilia
#8
Elvira D'Andrea, Tyra Lagerberg, Corrado De Vito, Erica Pitini, Carolina Marzuillo, Azzurra Massimi, Maria Rosaria Vacchio, Paola Grammatico, Paolo Villari
This article was originally published under an incorrect license. This has now been amended and is available under a CC BY-NC-ND 4.0 license. The PDF and HTML versions of the paper have been modified accordingly.
July 6, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29976978/genetic-diversity-of-ndufv1-dependent-mitochondrial-complex-i-deficiency
#9
Anshika Srivastava, Kinshuk Raj Srivastava, Malavika Hebbar, Chelna Galada, Rajagopal Kadavigrere, Fengyun Su, Xuhong Cao, Arul M Chinnaiyan, Katta M Girisha, Anju Shukla, Stephanie L Bielas
Medical genomics research performed in diverse population facilitates a better understanding of the genetic basis of developmental disorders, with regional implications for community genetics. Autosomal recessive mitochondrial complex I deficiency (MCID) accounts for a constellation of clinical features, including encephalopathies, myopathies, and Leigh Syndrome. Using whole-exome sequencing, we identified biallelic missense variants in NDUFV1 that encodes the 51-kD subunit of complex I (NADH dehydrogenase) NDUFV1...
July 5, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29976977/genome-wide-copy-number-variation-analysis-identifies-novel-candidate-loci-associated-with-pediatric-obesity
#10
Thanuja Selvanayagam, Susan Walker, Matthew J Gazzellone, Barbara Kellam, Cheryl Cytrynbaum, Dimitri J Stavropoulos, Ping Li, Catherine S Birken, Jill Hamilton, Rosanna Weksberg, Stephen W Scherer
Obesity is a multifactorial condition that is highly heritable. There have been ~60 susceptibility loci identified, but they only account for a fraction of cases. As copy number variations (CNVs) have been implicated in the etiology of a multitude of human disorders including obesity, here, we investigated the contribution of rare (<1% population frequency) CNVs in pediatric cases of obesity. We genotyped 67 such individuals, including 22 with co-morbid developmental delay and prioritized rare CNVs at known obesity-associated loci, as well as, those impacting genes involved in energy homeostasis or related processes...
July 5, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29976976/comparison-of-methods-for-transcriptome-imputation-through-application-to-two-common-complex-diseases
#11
James J Fryett, Jamie Inshaw, Andrew P Morris, Heather J Cordell
Transcriptome imputation has become a popular method for integrating genotype data with publicly available expression data to investigate the potentially causal role of genes in complex traits. Here, we compare three approaches (PrediXcan, MetaXcan and FUSION) via application to genome-wide association study (GWAS) data for Crohn's disease and type 1 diabetes from the Wellcome Trust Case Control Consortium. We investigate: (i) how the results of each approach compare with each other and with those of standard GWAS analysis; and (ii) how variants in the models used by the prediction tools compare with variants previously reported as eQTLs...
July 5, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29973660/could-the-interaction-between-lmx1b-and-pax2-influence-the-severity-of-renal-symptoms
#12
Susanna Negrisolo, Andrea Carraro, Giulia Fregonese, Elisa Benetti, Franz Schaefer, Marta Alberti, Salvatore Melchionda, Rita Fischetto, Mario Giordano, Luisa Murer
Nail Patella syndrome (NPS) is a rare autosomal dominant disease characterized by varying degrees of patella, nail, and elbows dysplasia and also ocular and renal congenital abnormalities. The renal involvement, ranging from hematuria and proteinuria to end-stage renal disease, is present in 22-60% of NPS cases. Heterozygous variants in LMX1B are known to be responsible of NPS and it has been hypothesized that the variable expressivity is due to the interaction of LMX1B with other developmental genes. We reported a case of co-presence of LMX1B and PAX2 variants in a child with extrarenal manifestation of NPS and end-stage renal disease but congenital bilateral renal hypodysplasia and vesicoureteral reflux...
July 4, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29970928/multi-level-genomic-analyses-suggest-new-genetic-variants-involved-in-human-memory
#13
Zijian Zhu, Biqing Chen, Hongming Yan, Wan Fang, Qin Zhou, Shanbi Zhou, Han Lei, Ailong Huang, Tingmei Chen, Tianming Gao, Liang Chen, Jieyu Chen, Dongsheng Ni, Yuping Gu, Jianing Liu, Wenxia Zhang, Yi Rao
Development of high-throughput genotyping platforms provides an opportunity to identify new genetic elements related to complex cognitive functions. Taking advantage of multi-level genomic analysis, here we studied the genetic basis of human short-term (STM, n = 1623) and long-term (LTM, n = 1522) memory functions. Heritability estimation based on single nucleotide polymorphism showed moderate (61%, standard error 35%) heritability of short-term memory but almost zero heritability of long-term memory...
July 3, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29970927/incidental-or-secondary-findings-an-integrative-and-patient-inclusive-approach-to-the-current-debate
#14
Marlies Saelaert, Heidi Mertes, Elfride De Baere, Ignaas Devisch
Incidental or secondary findings (ISFs) in whole exome or whole genome sequencing have been widely debated in recent literature. The American College of Medical Genetics and Genomics' recommendations on diagnostic ISFs have strongly catalyzed the discussion, resulting in worldwide reactions and a variety of international guidelines. This article will outline how propositions on levels of terminology, policy, and underlying values are still internationally criticized and adjusted. Unsolved questions regarding ISFs include a suitable terminology, adequate counseling or informed consent procedures, opt-out possibilities, reporting ISFs to (parents of) minors and values regarding professional duty, patient autonomy, and actionability...
July 3, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29967337/de-novo-repeat-interruptions-are-associated-with-reduced-somatic-instability-and-mild-or-absent-clinical-features-in-myotonic-dystrophy-type-1
#15
Sarah A Cumming, Mark J Hamilton, Yvonne Robb, Helen Gregory, Catherine McWilliam, Anneli Cooper, Berit Adam, Josephine McGhie, Graham Hamilton, Pawel Herzyk, Michael R Tschannen, Elizabeth Worthey, Richard Petty, Bob Ballantyne, Jon Warner, Maria Elena Farrugia, Cheryl Longman, Darren G Monckton
Myotonic dystrophy type 1 (DM1) is a multisystem disorder, caused by expansion of a CTG trinucleotide repeat in the 3'-untranslated region of the DMPK gene. The repeat expansion is somatically unstable and tends to increase in length with time, contributing to disease progression. In some individuals, the repeat array is interrupted by variant repeats such as CCG and CGG, stabilising the expansion and often leading to milder symptoms. We have characterised three families, each including one person with variant repeats that had arisen de novo on paternal transmission of the repeat expansion...
July 2, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29967336/optimization-of-the-diagnosis-of-inherited-colorectal-cancer-using-ngs-and-capture-of-exonic-and-intronic-sequences-of-panel-genes
#16
Stéphanie Baert-Desurmont, Sophie Coutant, Françoise Charbonnier, Pierre Macquere, François Lecoquierre, Mathias Schwartz, Maud Blanluet, Myriam Vezain, Raphaël Lanos, Olivier Quenez, Jacqueline Bou, Emilie Bouvignies, Steeve Fourneaux, Sandrine Manase, Stéphanie Vasseur, Jacques Mauillon, Marion Gerard, Régine Marlin, Gaëlle Bougeard, Julie Tinat, Thierry Frebourg, Isabelle Tournier
We have developed and validated for the diagnosis of inherited colorectal cancer (CRC) a massive parallel sequencing strategy based on: (i) fast capture of exonic and intronic sequences from ten genes involved in Mendelian forms of CRC (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, STK11, SMAD4, BMPR1A and PTEN); (ii) sequencing on MiSeq and NextSeq 500 Illumina platforms; (iii) a bioinformatic pipeline that includes BWA-Picard-GATK (Broad Institute) and CASAVA (Illumina) in parallel for mapping and variant calling, Alamut Batch (Interactive BioSoftware) for annotation, CANOES for CNV detection and finally, chimeric reads analysis for the detection of other types of structural variants (SVs)...
July 2, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29967335/pharmacogenomics-a-novel-section-in-the-european-journal-of-human-genetics
#17
EDITORIAL
Henk-Jan Guchelaar
No abstract text is available yet for this article.
July 2, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29967334/a-fine-mapping-study-of-central-obesity-loci-incorporating-functional-annotation-and-imputation
#18
Xiaoyu Zhang, L Adrienne Cupples, Ching-Ti Liu
A recent genome-wide association study (GWAS) of central obesity identified 27 loci, from sex-combined analysis, associated with waist-to-hip ratio adjusted for body-mass index (WHRadjBMI) in European-ancestry individuals. Nevertheless, the identified variants may not be the biological causal ones due to the presence of linkage disequilibrium (LD). To better understand the mechanisms underlying the identified loci from the GWAS meta-analysis, we first imputed summary statistics at GWAS loci to increase genetic resolution, and then we applied a Bayesian statistical fine-mapping method through PAINTOR, incorporating LD structure and functional annotations to select and prioritize the most plausible causal variants across WHRadjBMI-associated regions...
July 2, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29959382/whole-exome-sequencing-in-intellectual-disability-cost-before-and-after-a-diagnosis
#19
Terry Vrijenhoek, Eline M Middelburg, Glen R Monroe, Koen L I van Gassen, Joost W Geenen, Anke M Hövels, Nine V Knoers, Hans Kristian Ploos van Amstel, Gerardus W J Frederix
Clinical application of whole-exome and whole-genome sequencing (WES and WGS) has led to an increasing interest in how it could drive healthcare decisions. As with any healthcare innovation, implementation of next-generation sequencing in the clinic raises questions on affordability and costing impact for society as a whole. We retrospectively analyzed medical records of 370 patients with ID who had undergone WES at various stages of their diagnostic trajectory. We collected all medical interventions performed on these patients at the University Medical Center Utrecht (UMCU), Utrecht, the Netherlands...
June 29, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29955173/project-mine-study-design-and-pilot-analyses-of-a-large-scale-whole-genome-sequencing-study-in-amyotrophic-lateral-sclerosis
#20
(no author information available yet)
The most recent genome-wide association study in amyotrophic lateral sclerosis (ALS) demonstrates a disproportionate contribution from low-frequency variants to genetic susceptibility to disease. We have therefore begun Project MinE, an international collaboration that seeks to analyze whole-genome sequence data of at least 15 000 ALS patients and 7500 controls. Here, we report on the design of Project MinE and pilot analyses of successfully sequenced 1169 ALS patients and 608 controls drawn from the Netherlands...
June 28, 2018: European Journal of Human Genetics: EJHG
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